Global population genomics of two subspecies of<i>Cryptosporidium hominis</i>during 500 years of evolution

Tichkule, Swapnil; Cacciò, Simone M.; Robinson, Guy; Chalmers, Rachel M.; Müeller, Ivo; Emery-Corbin, Samantha J.; Eibach, Daniel; Oosterhout, Cock van; Jex, Aaron R.

doi:10.1101/2021.09.09.459610

Cited by 3 publications

(2 citation statements)

References 84 publications

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“…In some industrialized nations, such as the United States and Canada, most cases of human cryptosporidiosis are caused by C. hominis . Subtype IbA10G2 is the most frequently reported subtype of C. hominis, associated with several outbreaks in humans, and considered the major subtype responsible for infections in industrialized nations 22 - 24 . According to a previous study, the Ib subtype family was the most frequent in North America, followed by Ia, Id, and Ie 22 .…”

Section: Discussionmentioning

confidence: 99%

Prevalence of human cryptosporidiosis in the Americas: systematic review and meta-analysis

Jann

Cabral‐Castro

Costa

et al. 2022

Rev. Inst. Med. trop. S. Paulo

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Cryptosporidiosis is a disease caused by the Cryptosporidium spp parasite. As some species of Cryptosporidium have a wide host spectrum, the characterization of the pathogen at the species or genotype level is of great importance to define the sources of infection for humans and the potential for public health. This study investigated the diversity of the genus Cryptosporidium spp. in humans from all over the American continent and observed whether the method used to search for the parasite influenced the prevalence found in the Americas. This systematic review was carried out using the Pubmed, Science direct, Lilacs, Scielo, and Scopus databases with publications from January 1, 2010, to December 31, 2020. For data synthesis, the PRISMA flowchart was used and for the meta-analysis we used the MetaXL program. Of the selected publications, 57, 9 and 16 belonged to the region of South, Central and North America, respectively. The prevalence found for South, Central, and North America was 7%, 7%, and 8%, respectively, when analyzing publications that used only the microscopy method. When we analyzed the publications that used immunological and molecular methods, we found prevalences of 10%, 9%, and 21% for South, Central, and North America, respectively. The C. hominis subtype IbA10G2 was the most reported in the American continent, followed by subtype IeA11G3T3 and, for C. parvum, subtype IIaA15G2RI was the most reported. In conclusion, Cryptosporidium spp. is present throughout the American continent and its prevalence is higher when immunological and/or molecular methods are used, in addition to direct microscopic examination.

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Section: Discussionmentioning

confidence: 99%

Prevalence of human cryptosporidiosis in the Americas: systematic review and meta-analysis

Jann

Cabral‐Castro

Costa

et al. 2022

Rev. Inst. Med. trop. S. Paulo

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“…This is known to have resulted in the evolution of novel subspecies in other human parasites such as Cryptosporidium spp . (e.g., [5]), and such subspecies might continue to exchange genetic information that underpins their virulence evolution [6]. In the case of SARS-CoV-2, international travel is likely to contribute considerably to the gene flow of different variants across the globe, thereby increasing the probability of genetic introgression.…”

Section: Introductionmentioning

confidence: 99%

Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

Sant’Anna

Andreis

Salvato

et al. 2022

Preprint

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With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. This could result in the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of Spike gene (S). The 5' genome portion (circa 22 kb) resembles the AY.101 lineage (VOC Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 lineage (VOC Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, named AYBA-RS, is one out of almost 30 recombinants described this year. The submission of only four sequences in the GISAID database suggests that this Brazilian lineage had a minor epidemiological impact. On the other hand, the recent emergence of this and various other Deltacron recombinant lineages (i.e., XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that support this assertion, and we conclude that this stresses the need for continued genomic and epidemiological surveillance. This is particularly important for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.

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Evolutionary epidemiology of a zoonosis

Corsi

Tichkule²,

Sannella³

et al. 2021

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Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and all are likely recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

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Global population genomics of two subspecies ofCryptosporidium hominisduring 500 years of evolution

Cited by 3 publications

References 84 publications

Prevalence of human cryptosporidiosis in the Americas: systematic review and meta-analysis

Prevalence of human cryptosporidiosis in the Americas: systematic review and meta-analysis

Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

Evolutionary epidemiology of a zoonosis

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